Multiple sequence alignment - TraesCS4D01G245800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G245800 chr4D 100.000 2951 0 0 1 2951 414338232 414335282 0.000000e+00 5450.0
1 TraesCS4D01G245800 chr4D 97.149 2385 55 8 575 2951 414366038 414363659 0.000000e+00 4015.0
2 TraesCS4D01G245800 chr4D 90.878 1480 111 15 1021 2482 414359382 414357909 0.000000e+00 1964.0
3 TraesCS4D01G245800 chr4D 88.412 1096 106 11 872 1951 414328815 414327725 0.000000e+00 1301.0
4 TraesCS4D01G245800 chr4D 81.269 1009 160 20 1307 2312 414349728 414348746 0.000000e+00 789.0
5 TraesCS4D01G245800 chr4D 90.816 196 18 0 386 581 414366261 414366066 2.260000e-66 263.0
6 TraesCS4D01G245800 chr4D 81.633 147 17 6 575 719 414329162 414329024 2.400000e-21 113.0
7 TraesCS4D01G245800 chr4B 89.315 2059 163 32 575 2592 510563118 510561076 0.000000e+00 2531.0
8 TraesCS4D01G245800 chr4B 92.883 1686 78 20 575 2230 510482650 510480977 0.000000e+00 2410.0
9 TraesCS4D01G245800 chr4B 88.128 1095 109 11 872 1950 510435159 510434070 0.000000e+00 1282.0
10 TraesCS4D01G245800 chr4B 91.373 568 37 10 2269 2830 510480981 510480420 0.000000e+00 767.0
11 TraesCS4D01G245800 chr4B 79.592 1029 176 20 1318 2338 510530517 510529515 0.000000e+00 706.0
12 TraesCS4D01G245800 chr4B 94.000 250 14 1 332 581 510482926 510482678 7.720000e-101 377.0
13 TraesCS4D01G245800 chr4B 93.411 258 11 5 324 581 510563397 510563146 7.720000e-101 377.0
14 TraesCS4D01G245800 chr4B 82.723 191 17 10 575 760 510435475 510435296 3.940000e-34 156.0
15 TraesCS4D01G245800 chr4B 87.755 49 5 1 70 117 249115900 249115948 4.110000e-04 56.5
16 TraesCS4D01G245800 chr4B 87.500 48 5 1 70 116 249115849 249115896 1.000000e-03 54.7
17 TraesCS4D01G245800 chr4A 89.177 1506 119 26 1288 2784 49040330 49041800 0.000000e+00 1838.0
18 TraesCS4D01G245800 chr4A 89.381 1083 100 7 879 1951 49199669 49200746 0.000000e+00 1349.0
19 TraesCS4D01G245800 chr4A 90.446 628 37 6 575 1189 49039603 49040220 0.000000e+00 806.0
20 TraesCS4D01G245800 chr4A 89.552 201 19 1 383 581 49039375 49039575 1.360000e-63 254.0
21 TraesCS4D01G245800 chr4A 100.000 34 0 0 1174 1207 49040297 49040330 2.460000e-06 63.9
22 TraesCS4D01G245800 chr7D 97.231 325 9 0 1 325 127651226 127651550 4.300000e-153 551.0
23 TraesCS4D01G245800 chr2D 97.806 319 7 0 1 319 69348341 69348659 4.300000e-153 551.0
24 TraesCS4D01G245800 chr2B 86.170 188 18 5 68 248 744680388 744680574 2.320000e-46 196.0
25 TraesCS4D01G245800 chr5D 87.975 158 16 3 4 159 390689215 390689059 1.810000e-42 183.0
26 TraesCS4D01G245800 chr5B 86.486 148 19 1 13 159 471014904 471014757 8.460000e-36 161.0
27 TraesCS4D01G245800 chr3B 85.526 152 15 5 1001 1147 203613072 203613221 5.090000e-33 152.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G245800 chr4D 414335282 414338232 2950 True 5450.000000 5450 100.00000 1 2951 1 chr4D.!!$R1 2950
1 TraesCS4D01G245800 chr4D 414363659 414366261 2602 True 2139.000000 4015 93.98250 386 2951 2 chr4D.!!$R5 2565
2 TraesCS4D01G245800 chr4D 414357909 414359382 1473 True 1964.000000 1964 90.87800 1021 2482 1 chr4D.!!$R3 1461
3 TraesCS4D01G245800 chr4D 414348746 414349728 982 True 789.000000 789 81.26900 1307 2312 1 chr4D.!!$R2 1005
4 TraesCS4D01G245800 chr4D 414327725 414329162 1437 True 707.000000 1301 85.02250 575 1951 2 chr4D.!!$R4 1376
5 TraesCS4D01G245800 chr4B 510561076 510563397 2321 True 1454.000000 2531 91.36300 324 2592 2 chr4B.!!$R4 2268
6 TraesCS4D01G245800 chr4B 510480420 510482926 2506 True 1184.666667 2410 92.75200 332 2830 3 chr4B.!!$R3 2498
7 TraesCS4D01G245800 chr4B 510434070 510435475 1405 True 719.000000 1282 85.42550 575 1950 2 chr4B.!!$R2 1375
8 TraesCS4D01G245800 chr4B 510529515 510530517 1002 True 706.000000 706 79.59200 1318 2338 1 chr4B.!!$R1 1020
9 TraesCS4D01G245800 chr4A 49199669 49200746 1077 False 1349.000000 1349 89.38100 879 1951 1 chr4A.!!$F1 1072
10 TraesCS4D01G245800 chr4A 49039375 49041800 2425 False 740.475000 1838 92.29375 383 2784 4 chr4A.!!$F2 2401

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
150 151 0.041535 TGGGGATTGCAATGGAGCTT 59.958 50.0 18.59 0.0 34.99 3.74 F
200 201 0.098200 CTGCACTCGATGTTGCCATG 59.902 55.0 10.35 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1926 0.251209 GAACCTCACCCCACCTTTCC 60.251 60.000 0.0 0.0 0.0 3.13 R
2012 2287 2.929043 AGAAATTCCAACCATCCCTCCT 59.071 45.455 0.0 0.0 0.0 3.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.858433 CGCATCGCCGGGTCGTTA 62.858 66.667 2.18 0.00 0.00 3.18
29 30 2.960129 GCATCGCCGGGTCGTTAG 60.960 66.667 2.18 0.00 0.00 2.34
30 31 2.279252 CATCGCCGGGTCGTTAGG 60.279 66.667 2.18 0.00 0.00 2.69
31 32 4.217159 ATCGCCGGGTCGTTAGGC 62.217 66.667 2.18 0.00 46.88 3.93
35 36 4.077184 CCGGGTCGTTAGGCTGCA 62.077 66.667 0.50 0.00 0.00 4.41
36 37 2.047655 CGGGTCGTTAGGCTGCAA 60.048 61.111 0.50 0.00 0.00 4.08
37 38 1.449601 CGGGTCGTTAGGCTGCAAT 60.450 57.895 0.50 0.00 0.00 3.56
38 39 1.705337 CGGGTCGTTAGGCTGCAATG 61.705 60.000 0.50 0.00 0.00 2.82
39 40 1.376609 GGGTCGTTAGGCTGCAATGG 61.377 60.000 0.50 0.00 0.00 3.16
40 41 0.392461 GGTCGTTAGGCTGCAATGGA 60.392 55.000 0.50 0.00 0.00 3.41
41 42 1.009829 GTCGTTAGGCTGCAATGGAG 58.990 55.000 0.50 0.00 0.00 3.86
42 43 0.744414 TCGTTAGGCTGCAATGGAGC 60.744 55.000 18.67 18.67 35.57 4.70
43 44 0.745845 CGTTAGGCTGCAATGGAGCT 60.746 55.000 25.07 13.99 36.63 4.09
44 45 1.020437 GTTAGGCTGCAATGGAGCTC 58.980 55.000 25.07 15.47 36.63 4.09
45 46 0.107017 TTAGGCTGCAATGGAGCTCC 60.107 55.000 26.78 26.78 36.63 4.70
46 47 2.315781 TAGGCTGCAATGGAGCTCCG 62.316 60.000 27.43 14.68 39.43 4.63
47 48 3.885521 GCTGCAATGGAGCTCCGC 61.886 66.667 27.43 23.70 39.43 5.54
48 49 3.207669 CTGCAATGGAGCTCCGCC 61.208 66.667 27.43 15.25 39.43 6.13
51 52 4.473520 CAATGGAGCTCCGCCGGT 62.474 66.667 27.43 7.90 39.43 5.28
52 53 4.473520 AATGGAGCTCCGCCGGTG 62.474 66.667 27.43 8.42 39.43 4.94
55 56 4.899239 GGAGCTCCGCCGGTGATG 62.899 72.222 19.06 9.74 0.00 3.07
59 60 2.514592 CTCCGCCGGTGATGCATT 60.515 61.111 18.79 0.00 0.00 3.56
60 61 2.823593 TCCGCCGGTGATGCATTG 60.824 61.111 18.79 0.00 0.00 2.82
61 62 3.891400 CCGCCGGTGATGCATTGG 61.891 66.667 18.79 2.11 0.00 3.16
62 63 2.823593 CGCCGGTGATGCATTGGA 60.824 61.111 10.20 0.00 0.00 3.53
63 64 2.827051 CGCCGGTGATGCATTGGAG 61.827 63.158 10.20 0.00 0.00 3.86
64 65 3.113745 CCGGTGATGCATTGGAGC 58.886 61.111 0.00 0.00 0.00 4.70
65 66 2.711311 CGGTGATGCATTGGAGCG 59.289 61.111 0.00 6.09 37.31 5.03
66 67 2.410469 GGTGATGCATTGGAGCGC 59.590 61.111 0.00 0.00 37.31 5.92
67 68 2.117156 GGTGATGCATTGGAGCGCT 61.117 57.895 11.27 11.27 37.31 5.92
68 69 1.063649 GTGATGCATTGGAGCGCTG 59.936 57.895 18.48 0.53 37.31 5.18
69 70 1.377594 TGATGCATTGGAGCGCTGT 60.378 52.632 18.48 0.00 37.31 4.40
70 71 0.961857 TGATGCATTGGAGCGCTGTT 60.962 50.000 18.48 0.00 37.31 3.16
71 72 0.524816 GATGCATTGGAGCGCTGTTG 60.525 55.000 18.48 7.94 37.31 3.33
72 73 1.940883 ATGCATTGGAGCGCTGTTGG 61.941 55.000 18.48 0.71 37.31 3.77
73 74 2.629656 GCATTGGAGCGCTGTTGGT 61.630 57.895 18.48 0.00 0.00 3.67
74 75 1.210931 CATTGGAGCGCTGTTGGTG 59.789 57.895 18.48 3.00 0.00 4.17
80 81 4.268939 GCGCTGTTGGTGCTGCAA 62.269 61.111 2.77 0.00 46.82 4.08
81 82 2.646719 CGCTGTTGGTGCTGCAAT 59.353 55.556 2.77 0.00 33.72 3.56
82 83 1.731613 CGCTGTTGGTGCTGCAATG 60.732 57.895 2.77 0.00 33.72 2.82
83 84 1.373748 GCTGTTGGTGCTGCAATGG 60.374 57.895 2.77 0.00 34.18 3.16
84 85 1.808531 GCTGTTGGTGCTGCAATGGA 61.809 55.000 2.77 0.00 34.18 3.41
85 86 0.242825 CTGTTGGTGCTGCAATGGAG 59.757 55.000 2.77 0.00 0.00 3.86
86 87 1.080298 GTTGGTGCTGCAATGGAGC 60.080 57.895 19.99 19.99 36.95 4.70
87 88 1.228644 TTGGTGCTGCAATGGAGCT 60.229 52.632 26.10 0.00 37.35 4.09
88 89 0.828762 TTGGTGCTGCAATGGAGCTT 60.829 50.000 26.10 0.00 37.35 3.74
89 90 1.246056 TGGTGCTGCAATGGAGCTTC 61.246 55.000 26.10 18.24 37.35 3.86
90 91 1.136147 GTGCTGCAATGGAGCTTCG 59.864 57.895 26.10 0.00 37.35 3.79
91 92 2.101770 GCTGCAATGGAGCTTCGC 59.898 61.111 19.55 0.00 33.37 4.70
92 93 2.796651 CTGCAATGGAGCTTCGCC 59.203 61.111 0.00 0.00 34.99 5.54
93 94 3.104602 CTGCAATGGAGCTTCGCCG 62.105 63.158 0.00 0.00 34.99 6.46
94 95 3.880846 GCAATGGAGCTTCGCCGG 61.881 66.667 0.00 0.00 0.00 6.13
95 96 3.880846 CAATGGAGCTTCGCCGGC 61.881 66.667 19.07 19.07 0.00 6.13
113 114 4.374702 GTTGTCGGTGCTGCGCTG 62.375 66.667 15.68 15.68 0.00 5.18
124 125 4.669842 TGCGCTGCAGCTTCGTCT 62.670 61.111 34.22 0.00 39.32 4.18
125 126 3.847709 GCGCTGCAGCTTCGTCTC 61.848 66.667 34.22 11.79 39.32 3.36
126 127 3.540014 CGCTGCAGCTTCGTCTCG 61.540 66.667 34.22 14.00 39.32 4.04
127 128 3.847709 GCTGCAGCTTCGTCTCGC 61.848 66.667 31.33 0.78 38.21 5.03
128 129 3.184683 CTGCAGCTTCGTCTCGCC 61.185 66.667 0.00 0.00 0.00 5.54
129 130 4.742201 TGCAGCTTCGTCTCGCCC 62.742 66.667 0.00 0.00 0.00 6.13
131 132 3.764466 CAGCTTCGTCTCGCCCCT 61.764 66.667 0.00 0.00 0.00 4.79
132 133 3.764466 AGCTTCGTCTCGCCCCTG 61.764 66.667 0.00 0.00 0.00 4.45
133 134 4.821589 GCTTCGTCTCGCCCCTGG 62.822 72.222 0.00 0.00 0.00 4.45
134 135 4.148825 CTTCGTCTCGCCCCTGGG 62.149 72.222 5.50 5.50 38.57 4.45
145 146 3.959462 CCCTGGGGATTGCAATGG 58.041 61.111 18.59 11.19 37.50 3.16
146 147 1.310715 CCCTGGGGATTGCAATGGA 59.689 57.895 18.59 0.00 37.50 3.41
147 148 0.757935 CCCTGGGGATTGCAATGGAG 60.758 60.000 18.59 6.64 37.50 3.86
148 149 1.397390 CCTGGGGATTGCAATGGAGC 61.397 60.000 18.59 1.53 0.00 4.70
149 150 0.396695 CTGGGGATTGCAATGGAGCT 60.397 55.000 18.59 0.00 34.99 4.09
150 151 0.041535 TGGGGATTGCAATGGAGCTT 59.958 50.000 18.59 0.00 34.99 3.74
151 152 0.749049 GGGGATTGCAATGGAGCTTC 59.251 55.000 18.59 0.39 34.99 3.86
152 153 1.477553 GGGATTGCAATGGAGCTTCA 58.522 50.000 18.59 0.00 34.99 3.02
153 154 1.135721 GGGATTGCAATGGAGCTTCAC 59.864 52.381 18.59 0.00 34.99 3.18
154 155 1.135721 GGATTGCAATGGAGCTTCACC 59.864 52.381 18.59 4.38 34.99 4.02
155 156 1.820519 GATTGCAATGGAGCTTCACCA 59.179 47.619 18.59 0.00 41.83 4.17
156 157 1.250328 TTGCAATGGAGCTTCACCAG 58.750 50.000 0.00 0.00 40.89 4.00
157 158 0.609957 TGCAATGGAGCTTCACCAGG 60.610 55.000 0.00 0.00 40.89 4.45
158 159 1.318158 GCAATGGAGCTTCACCAGGG 61.318 60.000 0.00 0.00 40.89 4.45
159 160 0.329261 CAATGGAGCTTCACCAGGGA 59.671 55.000 0.00 0.00 40.89 4.20
160 161 0.622665 AATGGAGCTTCACCAGGGAG 59.377 55.000 0.00 0.00 40.89 4.30
161 162 1.277580 ATGGAGCTTCACCAGGGAGG 61.278 60.000 0.00 0.00 40.89 4.30
162 163 1.613630 GGAGCTTCACCAGGGAGGA 60.614 63.158 0.00 0.00 41.22 3.71
163 164 1.621672 GGAGCTTCACCAGGGAGGAG 61.622 65.000 0.00 0.00 41.22 3.69
164 165 1.614824 AGCTTCACCAGGGAGGAGG 60.615 63.158 0.00 0.00 41.22 4.30
165 166 2.674220 GCTTCACCAGGGAGGAGGG 61.674 68.421 0.00 0.00 41.22 4.30
166 167 1.997874 CTTCACCAGGGAGGAGGGG 60.998 68.421 0.00 0.00 41.22 4.79
167 168 3.579451 TTCACCAGGGAGGAGGGGG 62.579 68.421 0.00 0.00 41.22 5.40
168 169 4.354943 CACCAGGGAGGAGGGGGT 62.355 72.222 0.00 0.00 41.22 4.95
169 170 4.354943 ACCAGGGAGGAGGGGGTG 62.355 72.222 0.00 0.00 41.22 4.61
170 171 4.354943 CCAGGGAGGAGGGGGTGT 62.355 72.222 0.00 0.00 41.22 4.16
171 172 2.689034 CAGGGAGGAGGGGGTGTC 60.689 72.222 0.00 0.00 0.00 3.67
172 173 4.400251 AGGGAGGAGGGGGTGTCG 62.400 72.222 0.00 0.00 0.00 4.35
173 174 4.716977 GGGAGGAGGGGGTGTCGT 62.717 72.222 0.00 0.00 0.00 4.34
174 175 3.075641 GGAGGAGGGGGTGTCGTC 61.076 72.222 0.00 0.00 0.00 4.20
175 176 3.450115 GAGGAGGGGGTGTCGTCG 61.450 72.222 0.00 0.00 0.00 5.12
193 194 4.101448 GGGGGCTGCACTCGATGT 62.101 66.667 0.21 0.00 0.00 3.06
194 195 2.045926 GGGGCTGCACTCGATGTT 60.046 61.111 0.21 0.00 0.00 2.71
195 196 2.401766 GGGGCTGCACTCGATGTTG 61.402 63.158 0.21 0.00 0.00 3.33
196 197 2.482374 GGCTGCACTCGATGTTGC 59.518 61.111 0.50 6.81 0.00 4.17
197 198 2.482374 GCTGCACTCGATGTTGCC 59.518 61.111 10.35 0.00 0.00 4.52
198 199 2.327343 GCTGCACTCGATGTTGCCA 61.327 57.895 10.35 0.67 0.00 4.92
199 200 1.651240 GCTGCACTCGATGTTGCCAT 61.651 55.000 10.35 0.00 0.00 4.40
200 201 0.098200 CTGCACTCGATGTTGCCATG 59.902 55.000 10.35 0.00 0.00 3.66
201 202 1.307355 TGCACTCGATGTTGCCATGG 61.307 55.000 7.63 7.63 0.00 3.66
202 203 1.026182 GCACTCGATGTTGCCATGGA 61.026 55.000 18.40 0.00 34.98 3.41
203 204 1.671979 CACTCGATGTTGCCATGGAT 58.328 50.000 18.40 0.00 35.58 3.41
204 205 2.837498 CACTCGATGTTGCCATGGATA 58.163 47.619 18.40 0.00 35.58 2.59
205 206 2.804527 CACTCGATGTTGCCATGGATAG 59.195 50.000 18.40 0.00 35.58 2.08
206 207 1.802960 CTCGATGTTGCCATGGATAGC 59.197 52.381 18.40 6.11 35.58 2.97
207 208 1.140652 TCGATGTTGCCATGGATAGCA 59.859 47.619 18.40 12.13 31.72 3.49
208 209 1.265095 CGATGTTGCCATGGATAGCAC 59.735 52.381 18.40 4.09 39.10 4.40
209 210 1.265095 GATGTTGCCATGGATAGCACG 59.735 52.381 18.40 0.00 39.10 5.34
210 211 1.356624 GTTGCCATGGATAGCACGC 59.643 57.895 18.40 0.00 39.10 5.34
211 212 1.077858 TTGCCATGGATAGCACGCA 60.078 52.632 18.40 0.00 39.10 5.24
212 213 0.466007 TTGCCATGGATAGCACGCAT 60.466 50.000 18.40 0.00 39.10 4.73
213 214 0.886043 TGCCATGGATAGCACGCATC 60.886 55.000 18.40 0.00 33.08 3.91
214 215 1.904852 GCCATGGATAGCACGCATCG 61.905 60.000 18.40 0.00 0.00 3.84
215 216 1.293963 CCATGGATAGCACGCATCGG 61.294 60.000 5.56 0.00 0.00 4.18
216 217 1.669115 ATGGATAGCACGCATCGGC 60.669 57.895 0.00 0.00 0.00 5.54
217 218 2.029666 GGATAGCACGCATCGGCT 59.970 61.111 0.00 0.00 43.94 5.52
218 219 2.024319 GGATAGCACGCATCGGCTC 61.024 63.158 5.70 0.00 41.41 4.70
219 220 2.024319 GATAGCACGCATCGGCTCC 61.024 63.158 5.70 0.00 41.41 4.70
220 221 3.521529 ATAGCACGCATCGGCTCCC 62.522 63.158 5.70 0.00 41.41 4.30
239 240 4.819761 GTGCTGCGCCAGATCGGA 62.820 66.667 4.18 0.00 36.56 4.55
240 241 4.819761 TGCTGCGCCAGATCGGAC 62.820 66.667 4.18 0.44 36.56 4.79
242 243 4.498520 CTGCGCCAGATCGGACGT 62.499 66.667 4.18 0.00 36.86 4.34
243 244 3.989698 CTGCGCCAGATCGGACGTT 62.990 63.158 4.18 0.00 36.86 3.99
244 245 3.255379 GCGCCAGATCGGACGTTC 61.255 66.667 3.36 0.00 36.86 3.95
245 246 2.180769 CGCCAGATCGGACGTTCA 59.819 61.111 7.64 0.00 36.56 3.18
246 247 2.158959 CGCCAGATCGGACGTTCAC 61.159 63.158 7.64 0.00 36.56 3.18
247 248 1.810030 GCCAGATCGGACGTTCACC 60.810 63.158 7.64 0.00 36.56 4.02
248 249 1.589630 CCAGATCGGACGTTCACCA 59.410 57.895 0.00 0.00 36.56 4.17
249 250 0.458543 CCAGATCGGACGTTCACCAG 60.459 60.000 0.00 0.00 36.56 4.00
250 251 1.078759 CAGATCGGACGTTCACCAGC 61.079 60.000 0.00 0.00 0.00 4.85
251 252 2.126071 ATCGGACGTTCACCAGCG 60.126 61.111 0.00 0.00 0.00 5.18
252 253 2.814183 GATCGGACGTTCACCAGCGT 62.814 60.000 0.00 0.00 44.50 5.07
256 257 2.029073 ACGTTCACCAGCGTCCAG 59.971 61.111 0.00 0.00 36.54 3.86
257 258 2.338620 CGTTCACCAGCGTCCAGA 59.661 61.111 0.00 0.00 0.00 3.86
258 259 1.079819 CGTTCACCAGCGTCCAGAT 60.080 57.895 0.00 0.00 0.00 2.90
259 260 1.078759 CGTTCACCAGCGTCCAGATC 61.079 60.000 0.00 0.00 0.00 2.75
260 261 1.078759 GTTCACCAGCGTCCAGATCG 61.079 60.000 0.00 0.00 0.00 3.69
261 262 1.532604 TTCACCAGCGTCCAGATCGT 61.533 55.000 0.00 0.00 0.00 3.73
262 263 0.678684 TCACCAGCGTCCAGATCGTA 60.679 55.000 0.00 0.00 0.00 3.43
263 264 0.525668 CACCAGCGTCCAGATCGTAC 60.526 60.000 0.00 0.00 0.00 3.67
264 265 1.298413 CCAGCGTCCAGATCGTACG 60.298 63.158 9.53 9.53 39.55 3.67
265 266 1.298413 CAGCGTCCAGATCGTACGG 60.298 63.158 16.52 0.00 37.12 4.02
266 267 2.654404 GCGTCCAGATCGTACGGC 60.654 66.667 16.52 8.18 37.12 5.68
267 268 3.108343 CGTCCAGATCGTACGGCT 58.892 61.111 16.52 10.50 33.13 5.52
268 269 1.298413 CGTCCAGATCGTACGGCTG 60.298 63.158 23.36 23.36 33.13 4.85
270 271 3.207354 CCAGATCGTACGGCTGGT 58.793 61.111 32.11 11.90 43.25 4.00
271 272 1.515954 CCAGATCGTACGGCTGGTT 59.484 57.895 32.11 9.61 43.25 3.67
272 273 0.742505 CCAGATCGTACGGCTGGTTA 59.257 55.000 32.11 10.58 43.25 2.85
273 274 1.269102 CCAGATCGTACGGCTGGTTAG 60.269 57.143 32.11 17.64 43.25 2.34
274 275 1.030457 AGATCGTACGGCTGGTTAGG 58.970 55.000 16.52 0.00 0.00 2.69
275 276 0.596859 GATCGTACGGCTGGTTAGGC 60.597 60.000 16.52 0.00 45.44 3.93
281 282 2.908015 GGCTGGTTAGGCGGATGA 59.092 61.111 0.00 0.00 39.88 2.92
282 283 1.451936 GGCTGGTTAGGCGGATGAT 59.548 57.895 0.00 0.00 39.88 2.45
283 284 0.179018 GGCTGGTTAGGCGGATGATT 60.179 55.000 0.00 0.00 39.88 2.57
284 285 1.680338 GCTGGTTAGGCGGATGATTT 58.320 50.000 0.00 0.00 0.00 2.17
285 286 2.024414 GCTGGTTAGGCGGATGATTTT 58.976 47.619 0.00 0.00 0.00 1.82
286 287 2.033424 GCTGGTTAGGCGGATGATTTTC 59.967 50.000 0.00 0.00 0.00 2.29
287 288 3.545703 CTGGTTAGGCGGATGATTTTCT 58.454 45.455 0.00 0.00 0.00 2.52
288 289 3.278574 TGGTTAGGCGGATGATTTTCTG 58.721 45.455 0.00 0.00 0.00 3.02
289 290 2.033424 GGTTAGGCGGATGATTTTCTGC 59.967 50.000 0.00 0.00 45.47 4.26
293 294 2.634982 GCGGATGATTTTCTGCACAA 57.365 45.000 0.54 0.00 45.51 3.33
294 295 2.945278 GCGGATGATTTTCTGCACAAA 58.055 42.857 0.54 0.00 45.51 2.83
295 296 3.514645 GCGGATGATTTTCTGCACAAAT 58.485 40.909 0.54 0.00 45.51 2.32
296 297 3.549070 GCGGATGATTTTCTGCACAAATC 59.451 43.478 15.46 15.46 45.51 2.17
301 302 4.735985 TGATTTTCTGCACAAATCATCCG 58.264 39.130 19.03 0.00 42.90 4.18
302 303 4.458642 TGATTTTCTGCACAAATCATCCGA 59.541 37.500 19.03 3.60 42.90 4.55
303 304 3.829886 TTTCTGCACAAATCATCCGAC 57.170 42.857 0.00 0.00 0.00 4.79
304 305 2.768253 TCTGCACAAATCATCCGACT 57.232 45.000 0.00 0.00 0.00 4.18
305 306 3.057969 TCTGCACAAATCATCCGACTT 57.942 42.857 0.00 0.00 0.00 3.01
306 307 4.200838 TCTGCACAAATCATCCGACTTA 57.799 40.909 0.00 0.00 0.00 2.24
307 308 4.769688 TCTGCACAAATCATCCGACTTAT 58.230 39.130 0.00 0.00 0.00 1.73
308 309 4.811024 TCTGCACAAATCATCCGACTTATC 59.189 41.667 0.00 0.00 0.00 1.75
309 310 3.876914 TGCACAAATCATCCGACTTATCC 59.123 43.478 0.00 0.00 0.00 2.59
310 311 3.059597 GCACAAATCATCCGACTTATCCG 60.060 47.826 0.00 0.00 0.00 4.18
311 312 4.119862 CACAAATCATCCGACTTATCCGT 58.880 43.478 0.00 0.00 0.00 4.69
312 313 5.286438 CACAAATCATCCGACTTATCCGTA 58.714 41.667 0.00 0.00 0.00 4.02
313 314 5.402568 CACAAATCATCCGACTTATCCGTAG 59.597 44.000 0.00 0.00 0.00 3.51
314 315 5.068723 ACAAATCATCCGACTTATCCGTAGT 59.931 40.000 0.00 0.00 0.00 2.73
315 316 6.263842 ACAAATCATCCGACTTATCCGTAGTA 59.736 38.462 0.00 0.00 0.00 1.82
316 317 6.497785 AATCATCCGACTTATCCGTAGTAG 57.502 41.667 0.00 0.00 0.00 2.57
317 318 3.750130 TCATCCGACTTATCCGTAGTAGC 59.250 47.826 0.00 0.00 0.00 3.58
318 319 2.498167 TCCGACTTATCCGTAGTAGCC 58.502 52.381 0.00 0.00 0.00 3.93
319 320 2.158769 TCCGACTTATCCGTAGTAGCCA 60.159 50.000 0.00 0.00 0.00 4.75
320 321 2.031333 CCGACTTATCCGTAGTAGCCAC 60.031 54.545 0.00 0.00 0.00 5.01
321 322 2.031333 CGACTTATCCGTAGTAGCCACC 60.031 54.545 0.00 0.00 0.00 4.61
322 323 3.220940 GACTTATCCGTAGTAGCCACCT 58.779 50.000 0.00 0.00 0.00 4.00
323 324 3.635836 GACTTATCCGTAGTAGCCACCTT 59.364 47.826 0.00 0.00 0.00 3.50
324 325 4.028825 ACTTATCCGTAGTAGCCACCTTT 58.971 43.478 0.00 0.00 0.00 3.11
325 326 4.468868 ACTTATCCGTAGTAGCCACCTTTT 59.531 41.667 0.00 0.00 0.00 2.27
326 327 3.994931 ATCCGTAGTAGCCACCTTTTT 57.005 42.857 0.00 0.00 0.00 1.94
381 382 8.318412 AGGTTTGTGCTTTATTTATAAAAGGGG 58.682 33.333 1.21 0.00 35.04 4.79
474 477 2.913777 GAACAAGCCATTACGTTCCC 57.086 50.000 0.00 0.00 33.27 3.97
483 486 0.179056 ATTACGTTCCCTCATGCCGG 60.179 55.000 0.00 0.00 0.00 6.13
560 563 1.086634 GCAGACGCATCCTTCCTCAC 61.087 60.000 0.00 0.00 38.36 3.51
563 566 1.078759 GACGCATCCTTCCTCACACG 61.079 60.000 0.00 0.00 0.00 4.49
583 620 1.261619 GAAGGGACGCAGCAAATATCG 59.738 52.381 0.00 0.00 0.00 2.92
667 716 6.810182 TCAGAAAGTGTTAAGCTAATACCGAC 59.190 38.462 0.00 0.00 31.07 4.79
670 726 5.511234 AGTGTTAAGCTAATACCGACGAT 57.489 39.130 0.00 0.00 31.07 3.73
763 854 1.052617 TAGCCCGTAAGCCATGCATA 58.947 50.000 0.00 0.00 0.00 3.14
817 913 1.227883 CTAGCCCGCCTCTCTCGTA 60.228 63.158 0.00 0.00 0.00 3.43
895 1035 7.496346 AACTATGAGAACCAAATCCTCACTA 57.504 36.000 0.00 0.00 39.43 2.74
938 1093 0.466189 ACAACACACAGCTTCCCAGG 60.466 55.000 0.00 0.00 0.00 4.45
999 1162 4.528674 GCATCCAGCGACAGACAT 57.471 55.556 0.00 0.00 0.00 3.06
1003 1166 2.546584 GCATCCAGCGACAGACATATGA 60.547 50.000 10.38 0.00 0.00 2.15
1048 1211 2.917227 TGGTGGCTCTCGTGCTCA 60.917 61.111 0.00 0.00 0.00 4.26
1278 1541 2.314246 GGGTACGGCAACCTATACTCT 58.686 52.381 6.03 0.00 39.65 3.24
1356 1619 1.577468 CGTGTGGTCAGTGCTACAAA 58.423 50.000 5.57 0.00 31.82 2.83
1655 1926 2.401766 GCAGGGTTCCATGCGTGAG 61.402 63.158 12.50 0.00 31.87 3.51
2012 2287 4.751767 TGTGAGCATACCATCATACACA 57.248 40.909 0.00 0.00 35.24 3.72
2058 2333 9.482627 CTTTATTTATGGTGTGGTGCTTAAAAA 57.517 29.630 0.00 0.00 0.00 1.94
2866 3174 5.636123 TGGCCTAGTTTTTCCTCATAAACA 58.364 37.500 3.32 0.00 36.85 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.858433 TAACGACCCGGCGATGCG 62.858 66.667 9.30 11.18 34.83 4.73
12 13 2.960129 CTAACGACCCGGCGATGC 60.960 66.667 9.30 0.00 34.83 3.91
13 14 2.279252 CCTAACGACCCGGCGATG 60.279 66.667 9.30 0.68 34.83 3.84
14 15 4.217159 GCCTAACGACCCGGCGAT 62.217 66.667 9.30 0.00 33.64 4.58
18 19 2.869503 ATTGCAGCCTAACGACCCGG 62.870 60.000 0.00 0.00 0.00 5.73
19 20 1.449601 ATTGCAGCCTAACGACCCG 60.450 57.895 0.00 0.00 0.00 5.28
20 21 1.376609 CCATTGCAGCCTAACGACCC 61.377 60.000 0.00 0.00 0.00 4.46
21 22 0.392461 TCCATTGCAGCCTAACGACC 60.392 55.000 0.00 0.00 0.00 4.79
22 23 1.009829 CTCCATTGCAGCCTAACGAC 58.990 55.000 0.00 0.00 0.00 4.34
23 24 0.744414 GCTCCATTGCAGCCTAACGA 60.744 55.000 0.00 0.00 0.00 3.85
24 25 0.745845 AGCTCCATTGCAGCCTAACG 60.746 55.000 0.00 0.00 37.63 3.18
25 26 1.020437 GAGCTCCATTGCAGCCTAAC 58.980 55.000 0.87 0.00 37.63 2.34
26 27 0.107017 GGAGCTCCATTGCAGCCTAA 60.107 55.000 28.43 0.00 37.63 2.69
27 28 1.528824 GGAGCTCCATTGCAGCCTA 59.471 57.895 28.43 0.00 37.63 3.93
28 29 2.274760 GGAGCTCCATTGCAGCCT 59.725 61.111 28.43 0.00 37.63 4.58
29 30 3.207669 CGGAGCTCCATTGCAGCC 61.208 66.667 31.67 2.66 37.63 4.85
42 43 2.514592 AATGCATCACCGGCGGAG 60.515 61.111 35.78 26.54 0.00 4.63
43 44 2.823593 CAATGCATCACCGGCGGA 60.824 61.111 35.78 12.34 0.00 5.54
44 45 3.891400 CCAATGCATCACCGGCGG 61.891 66.667 27.06 27.06 0.00 6.13
45 46 2.823593 TCCAATGCATCACCGGCG 60.824 61.111 0.00 0.00 0.00 6.46
46 47 3.113745 CTCCAATGCATCACCGGC 58.886 61.111 0.00 0.00 0.00 6.13
47 48 2.827051 CGCTCCAATGCATCACCGG 61.827 63.158 0.00 0.00 0.00 5.28
48 49 2.711311 CGCTCCAATGCATCACCG 59.289 61.111 0.00 0.00 0.00 4.94
49 50 2.117156 AGCGCTCCAATGCATCACC 61.117 57.895 2.64 0.00 0.00 4.02
50 51 1.063649 CAGCGCTCCAATGCATCAC 59.936 57.895 7.13 0.00 0.00 3.06
51 52 0.961857 AACAGCGCTCCAATGCATCA 60.962 50.000 7.13 0.00 0.00 3.07
52 53 0.524816 CAACAGCGCTCCAATGCATC 60.525 55.000 7.13 0.00 0.00 3.91
53 54 1.509463 CAACAGCGCTCCAATGCAT 59.491 52.632 7.13 0.00 0.00 3.96
54 55 2.628696 CCAACAGCGCTCCAATGCA 61.629 57.895 7.13 0.00 0.00 3.96
55 56 2.180017 CCAACAGCGCTCCAATGC 59.820 61.111 7.13 0.00 0.00 3.56
56 57 1.210931 CACCAACAGCGCTCCAATG 59.789 57.895 7.13 3.92 0.00 2.82
57 58 2.629656 GCACCAACAGCGCTCCAAT 61.630 57.895 7.13 0.00 0.00 3.16
58 59 3.286751 GCACCAACAGCGCTCCAA 61.287 61.111 7.13 0.00 0.00 3.53
59 60 4.254709 AGCACCAACAGCGCTCCA 62.255 61.111 7.13 0.00 37.01 3.86
60 61 3.730761 CAGCACCAACAGCGCTCC 61.731 66.667 7.13 0.00 37.01 4.70
61 62 4.395583 GCAGCACCAACAGCGCTC 62.396 66.667 7.13 0.00 37.01 5.03
63 64 3.562779 ATTGCAGCACCAACAGCGC 62.563 57.895 0.00 0.00 37.01 5.92
64 65 1.731613 CATTGCAGCACCAACAGCG 60.732 57.895 0.00 0.00 37.01 5.18
65 66 1.373748 CCATTGCAGCACCAACAGC 60.374 57.895 0.00 0.00 0.00 4.40
66 67 0.242825 CTCCATTGCAGCACCAACAG 59.757 55.000 0.00 0.00 0.00 3.16
67 68 1.808531 GCTCCATTGCAGCACCAACA 61.809 55.000 0.00 0.00 36.82 3.33
68 69 1.080298 GCTCCATTGCAGCACCAAC 60.080 57.895 0.00 0.00 36.82 3.77
69 70 0.828762 AAGCTCCATTGCAGCACCAA 60.829 50.000 1.78 0.00 39.56 3.67
70 71 1.228644 AAGCTCCATTGCAGCACCA 60.229 52.632 1.78 0.00 39.56 4.17
71 72 1.509923 GAAGCTCCATTGCAGCACC 59.490 57.895 1.78 0.00 39.56 5.01
72 73 1.136147 CGAAGCTCCATTGCAGCAC 59.864 57.895 1.78 0.00 39.56 4.40
73 74 3.582148 CGAAGCTCCATTGCAGCA 58.418 55.556 1.78 0.00 39.56 4.41
110 111 3.847709 GCGAGACGAAGCTGCAGC 61.848 66.667 31.53 31.53 42.49 5.25
111 112 3.184683 GGCGAGACGAAGCTGCAG 61.185 66.667 10.11 10.11 0.00 4.41
112 113 4.742201 GGGCGAGACGAAGCTGCA 62.742 66.667 1.02 0.00 0.00 4.41
114 115 3.764466 AGGGGCGAGACGAAGCTG 61.764 66.667 0.00 0.00 0.00 4.24
115 116 3.764466 CAGGGGCGAGACGAAGCT 61.764 66.667 0.00 0.00 0.00 3.74
116 117 4.821589 CCAGGGGCGAGACGAAGC 62.822 72.222 0.00 0.00 0.00 3.86
117 118 4.148825 CCCAGGGGCGAGACGAAG 62.149 72.222 0.00 0.00 0.00 3.79
121 122 3.090532 AATCCCCAGGGGCGAGAC 61.091 66.667 21.90 0.00 43.94 3.36
122 123 3.089874 CAATCCCCAGGGGCGAGA 61.090 66.667 21.90 2.04 43.94 4.04
123 124 4.883354 GCAATCCCCAGGGGCGAG 62.883 72.222 21.90 12.48 43.94 5.03
125 126 4.757355 TTGCAATCCCCAGGGGCG 62.757 66.667 21.90 11.87 43.94 6.13
126 127 2.041612 ATTGCAATCCCCAGGGGC 60.042 61.111 21.90 8.75 43.94 5.80
127 128 1.763256 CCATTGCAATCCCCAGGGG 60.763 63.158 20.55 20.55 46.11 4.79
128 129 0.757935 CTCCATTGCAATCCCCAGGG 60.758 60.000 9.53 6.93 0.00 4.45
129 130 1.397390 GCTCCATTGCAATCCCCAGG 61.397 60.000 9.53 7.70 0.00 4.45
130 131 0.396695 AGCTCCATTGCAATCCCCAG 60.397 55.000 9.53 4.18 34.99 4.45
131 132 0.041535 AAGCTCCATTGCAATCCCCA 59.958 50.000 9.53 0.00 34.99 4.96
132 133 0.749049 GAAGCTCCATTGCAATCCCC 59.251 55.000 9.53 0.00 34.99 4.81
133 134 1.135721 GTGAAGCTCCATTGCAATCCC 59.864 52.381 9.53 0.00 34.99 3.85
134 135 1.135721 GGTGAAGCTCCATTGCAATCC 59.864 52.381 9.53 0.27 34.99 3.01
135 136 1.820519 TGGTGAAGCTCCATTGCAATC 59.179 47.619 9.53 0.00 34.99 2.67
136 137 1.822990 CTGGTGAAGCTCCATTGCAAT 59.177 47.619 5.99 5.99 34.26 3.56
137 138 1.250328 CTGGTGAAGCTCCATTGCAA 58.750 50.000 0.00 0.00 34.26 4.08
138 139 0.609957 CCTGGTGAAGCTCCATTGCA 60.610 55.000 0.00 0.00 34.26 4.08
139 140 1.318158 CCCTGGTGAAGCTCCATTGC 61.318 60.000 0.00 0.00 34.26 3.56
140 141 0.329261 TCCCTGGTGAAGCTCCATTG 59.671 55.000 0.00 0.00 34.26 2.82
141 142 0.622665 CTCCCTGGTGAAGCTCCATT 59.377 55.000 0.00 0.00 34.26 3.16
142 143 1.277580 CCTCCCTGGTGAAGCTCCAT 61.278 60.000 0.00 0.00 34.26 3.41
143 144 1.920325 CCTCCCTGGTGAAGCTCCA 60.920 63.158 0.00 0.00 0.00 3.86
144 145 1.613630 TCCTCCCTGGTGAAGCTCC 60.614 63.158 0.00 0.00 37.07 4.70
145 146 1.621672 CCTCCTCCCTGGTGAAGCTC 61.622 65.000 0.00 0.00 37.07 4.09
146 147 1.614824 CCTCCTCCCTGGTGAAGCT 60.615 63.158 0.00 0.00 37.07 3.74
147 148 2.674220 CCCTCCTCCCTGGTGAAGC 61.674 68.421 0.00 0.00 37.07 3.86
148 149 1.997874 CCCCTCCTCCCTGGTGAAG 60.998 68.421 0.00 0.00 37.07 3.02
149 150 2.124996 CCCCTCCTCCCTGGTGAA 59.875 66.667 0.00 0.00 37.07 3.18
150 151 4.024984 CCCCCTCCTCCCTGGTGA 62.025 72.222 0.00 0.00 37.07 4.02
151 152 4.354943 ACCCCCTCCTCCCTGGTG 62.355 72.222 0.00 0.00 37.07 4.17
152 153 4.354943 CACCCCCTCCTCCCTGGT 62.355 72.222 0.00 0.00 37.07 4.00
153 154 4.354943 ACACCCCCTCCTCCCTGG 62.355 72.222 0.00 0.00 37.10 4.45
154 155 2.689034 GACACCCCCTCCTCCCTG 60.689 72.222 0.00 0.00 0.00 4.45
155 156 4.400251 CGACACCCCCTCCTCCCT 62.400 72.222 0.00 0.00 0.00 4.20
156 157 4.716977 ACGACACCCCCTCCTCCC 62.717 72.222 0.00 0.00 0.00 4.30
157 158 3.075641 GACGACACCCCCTCCTCC 61.076 72.222 0.00 0.00 0.00 4.30
158 159 3.450115 CGACGACACCCCCTCCTC 61.450 72.222 0.00 0.00 0.00 3.71
176 177 3.628646 AACATCGAGTGCAGCCCCC 62.629 63.158 0.00 0.00 0.00 5.40
177 178 2.045926 AACATCGAGTGCAGCCCC 60.046 61.111 0.00 0.00 0.00 5.80
178 179 3.044059 GCAACATCGAGTGCAGCCC 62.044 63.158 12.25 0.00 0.00 5.19
179 180 2.482374 GCAACATCGAGTGCAGCC 59.518 61.111 12.25 0.00 0.00 4.85
180 181 2.327343 TGGCAACATCGAGTGCAGC 61.327 57.895 17.24 10.51 46.17 5.25
181 182 3.970721 TGGCAACATCGAGTGCAG 58.029 55.556 17.24 3.04 46.17 4.41
192 193 1.356624 GCGTGCTATCCATGGCAAC 59.643 57.895 6.96 0.00 45.91 4.17
193 194 0.466007 ATGCGTGCTATCCATGGCAA 60.466 50.000 6.96 0.00 45.91 4.52
194 195 0.886043 GATGCGTGCTATCCATGGCA 60.886 55.000 6.96 0.00 42.18 4.92
195 196 1.871772 GATGCGTGCTATCCATGGC 59.128 57.895 6.96 0.00 34.56 4.40
196 197 1.293963 CCGATGCGTGCTATCCATGG 61.294 60.000 4.97 4.97 0.00 3.66
197 198 1.904852 GCCGATGCGTGCTATCCATG 61.905 60.000 0.00 0.00 0.00 3.66
198 199 1.669115 GCCGATGCGTGCTATCCAT 60.669 57.895 0.00 0.00 0.00 3.41
199 200 2.280119 GCCGATGCGTGCTATCCA 60.280 61.111 0.00 0.00 0.00 3.41
200 201 2.024319 GAGCCGATGCGTGCTATCC 61.024 63.158 0.00 0.00 44.33 2.59
201 202 2.024319 GGAGCCGATGCGTGCTATC 61.024 63.158 0.00 0.00 44.33 2.08
202 203 2.029666 GGAGCCGATGCGTGCTAT 59.970 61.111 0.00 0.00 44.33 2.97
203 204 4.221422 GGGAGCCGATGCGTGCTA 62.221 66.667 0.00 0.00 44.33 3.49
225 226 3.989698 AACGTCCGATCTGGCGCAG 62.990 63.158 10.83 4.99 39.77 5.18
226 227 3.982372 GAACGTCCGATCTGGCGCA 62.982 63.158 10.83 0.00 39.77 6.09
227 228 3.255379 GAACGTCCGATCTGGCGC 61.255 66.667 11.24 0.00 39.77 6.53
228 229 2.158959 GTGAACGTCCGATCTGGCG 61.159 63.158 9.72 9.72 41.23 5.69
229 230 1.810030 GGTGAACGTCCGATCTGGC 60.810 63.158 0.00 0.00 37.80 4.85
230 231 0.458543 CTGGTGAACGTCCGATCTGG 60.459 60.000 0.00 0.00 40.09 3.86
231 232 1.078759 GCTGGTGAACGTCCGATCTG 61.079 60.000 0.00 0.00 0.00 2.90
232 233 1.215647 GCTGGTGAACGTCCGATCT 59.784 57.895 0.00 0.00 0.00 2.75
233 234 2.158959 CGCTGGTGAACGTCCGATC 61.159 63.158 0.00 0.00 0.00 3.69
234 235 2.126071 CGCTGGTGAACGTCCGAT 60.126 61.111 0.00 0.00 0.00 4.18
235 236 3.598715 ACGCTGGTGAACGTCCGA 61.599 61.111 0.00 0.00 38.28 4.55
239 240 1.816863 ATCTGGACGCTGGTGAACGT 61.817 55.000 0.00 0.00 46.91 3.99
240 241 1.078759 GATCTGGACGCTGGTGAACG 61.079 60.000 0.00 0.00 0.00 3.95
241 242 1.078759 CGATCTGGACGCTGGTGAAC 61.079 60.000 0.00 0.00 0.00 3.18
242 243 1.215382 CGATCTGGACGCTGGTGAA 59.785 57.895 0.00 0.00 0.00 3.18
243 244 0.678684 TACGATCTGGACGCTGGTGA 60.679 55.000 0.00 0.00 0.00 4.02
244 245 0.525668 GTACGATCTGGACGCTGGTG 60.526 60.000 0.00 0.00 0.00 4.17
245 246 1.807886 GTACGATCTGGACGCTGGT 59.192 57.895 0.00 0.00 0.00 4.00
246 247 1.298413 CGTACGATCTGGACGCTGG 60.298 63.158 10.44 0.00 0.00 4.85
247 248 1.298413 CCGTACGATCTGGACGCTG 60.298 63.158 18.76 1.92 35.28 5.18
248 249 3.108343 CCGTACGATCTGGACGCT 58.892 61.111 18.76 0.00 35.28 5.07
249 250 2.654404 GCCGTACGATCTGGACGC 60.654 66.667 18.76 4.86 35.28 5.19
250 251 1.298413 CAGCCGTACGATCTGGACG 60.298 63.158 18.76 13.24 36.36 4.79
251 252 4.711980 CAGCCGTACGATCTGGAC 57.288 61.111 18.76 0.00 0.00 4.02
254 255 1.269102 CCTAACCAGCCGTACGATCTG 60.269 57.143 18.76 21.05 0.00 2.90
255 256 1.030457 CCTAACCAGCCGTACGATCT 58.970 55.000 18.76 10.51 0.00 2.75
256 257 0.596859 GCCTAACCAGCCGTACGATC 60.597 60.000 18.76 8.14 0.00 3.69
257 258 1.440476 GCCTAACCAGCCGTACGAT 59.560 57.895 18.76 1.33 0.00 3.73
258 259 2.887360 GCCTAACCAGCCGTACGA 59.113 61.111 18.76 0.00 0.00 3.43
259 260 2.581409 CGCCTAACCAGCCGTACG 60.581 66.667 8.69 8.69 0.00 3.67
260 261 2.024590 ATCCGCCTAACCAGCCGTAC 62.025 60.000 0.00 0.00 0.00 3.67
261 262 1.759299 ATCCGCCTAACCAGCCGTA 60.759 57.895 0.00 0.00 0.00 4.02
262 263 3.081409 ATCCGCCTAACCAGCCGT 61.081 61.111 0.00 0.00 0.00 5.68
263 264 2.383245 ATCATCCGCCTAACCAGCCG 62.383 60.000 0.00 0.00 0.00 5.52
264 265 0.179018 AATCATCCGCCTAACCAGCC 60.179 55.000 0.00 0.00 0.00 4.85
265 266 1.680338 AAATCATCCGCCTAACCAGC 58.320 50.000 0.00 0.00 0.00 4.85
266 267 3.313526 CAGAAAATCATCCGCCTAACCAG 59.686 47.826 0.00 0.00 0.00 4.00
267 268 3.278574 CAGAAAATCATCCGCCTAACCA 58.721 45.455 0.00 0.00 0.00 3.67
268 269 2.033424 GCAGAAAATCATCCGCCTAACC 59.967 50.000 0.00 0.00 0.00 2.85
269 270 2.682856 TGCAGAAAATCATCCGCCTAAC 59.317 45.455 0.00 0.00 0.00 2.34
270 271 2.682856 GTGCAGAAAATCATCCGCCTAA 59.317 45.455 0.00 0.00 0.00 2.69
271 272 2.288666 GTGCAGAAAATCATCCGCCTA 58.711 47.619 0.00 0.00 0.00 3.93
272 273 1.098050 GTGCAGAAAATCATCCGCCT 58.902 50.000 0.00 0.00 0.00 5.52
273 274 0.810648 TGTGCAGAAAATCATCCGCC 59.189 50.000 0.00 0.00 0.00 6.13
274 275 2.634982 TTGTGCAGAAAATCATCCGC 57.365 45.000 0.00 0.00 0.00 5.54
275 276 4.735985 TGATTTGTGCAGAAAATCATCCG 58.264 39.130 23.89 0.00 44.86 4.18
280 281 4.795278 GTCGGATGATTTGTGCAGAAAATC 59.205 41.667 20.52 20.52 42.07 2.17
281 282 4.460382 AGTCGGATGATTTGTGCAGAAAAT 59.540 37.500 13.53 9.87 0.00 1.82
282 283 3.820467 AGTCGGATGATTTGTGCAGAAAA 59.180 39.130 13.53 5.02 0.00 2.29
283 284 3.411446 AGTCGGATGATTTGTGCAGAAA 58.589 40.909 11.84 11.84 0.00 2.52
284 285 3.057969 AGTCGGATGATTTGTGCAGAA 57.942 42.857 0.00 0.00 0.00 3.02
285 286 2.768253 AGTCGGATGATTTGTGCAGA 57.232 45.000 0.00 0.00 0.00 4.26
286 287 4.024556 GGATAAGTCGGATGATTTGTGCAG 60.025 45.833 0.00 0.00 0.00 4.41
287 288 3.876914 GGATAAGTCGGATGATTTGTGCA 59.123 43.478 0.00 0.00 0.00 4.57
288 289 3.059597 CGGATAAGTCGGATGATTTGTGC 60.060 47.826 0.00 0.00 0.00 4.57
289 290 4.119862 ACGGATAAGTCGGATGATTTGTG 58.880 43.478 0.00 0.00 0.00 3.33
290 291 4.402056 ACGGATAAGTCGGATGATTTGT 57.598 40.909 0.00 0.00 0.00 2.83
291 292 5.529791 ACTACGGATAAGTCGGATGATTTG 58.470 41.667 0.00 0.00 0.00 2.32
292 293 5.786264 ACTACGGATAAGTCGGATGATTT 57.214 39.130 0.00 0.00 0.00 2.17
293 294 5.106237 GCTACTACGGATAAGTCGGATGATT 60.106 44.000 0.00 0.00 0.00 2.57
294 295 4.395542 GCTACTACGGATAAGTCGGATGAT 59.604 45.833 0.00 0.00 0.00 2.45
295 296 3.750130 GCTACTACGGATAAGTCGGATGA 59.250 47.826 0.00 0.00 0.00 2.92
296 297 3.119919 GGCTACTACGGATAAGTCGGATG 60.120 52.174 0.00 0.00 0.00 3.51
297 298 3.080319 GGCTACTACGGATAAGTCGGAT 58.920 50.000 0.00 0.00 0.00 4.18
298 299 2.158769 TGGCTACTACGGATAAGTCGGA 60.159 50.000 0.00 0.00 0.00 4.55
299 300 2.031333 GTGGCTACTACGGATAAGTCGG 60.031 54.545 0.00 0.00 0.00 4.79
300 301 2.031333 GGTGGCTACTACGGATAAGTCG 60.031 54.545 0.00 0.00 0.00 4.18
301 302 3.220940 AGGTGGCTACTACGGATAAGTC 58.779 50.000 0.00 0.00 0.00 3.01
302 303 3.309600 AGGTGGCTACTACGGATAAGT 57.690 47.619 0.00 0.00 0.00 2.24
303 304 4.667519 AAAGGTGGCTACTACGGATAAG 57.332 45.455 0.00 0.00 0.00 1.73
304 305 5.425196 AAAAAGGTGGCTACTACGGATAA 57.575 39.130 0.00 0.00 0.00 1.75
306 307 3.994931 AAAAAGGTGGCTACTACGGAT 57.005 42.857 0.00 0.00 0.00 4.18
342 343 3.484683 CACAAACCTTAAATACACCGCG 58.515 45.455 0.00 0.00 0.00 6.46
345 346 9.483916 AAATAAAGCACAAACCTTAAATACACC 57.516 29.630 0.00 0.00 0.00 4.16
374 375 3.749284 AAGGTGCGTGGCCCCTTTT 62.749 57.895 0.00 0.00 34.99 2.27
499 502 2.125106 GCCGCACCTGGTCCTAAG 60.125 66.667 0.00 0.00 0.00 2.18
560 563 1.577328 ATTTGCTGCGTCCCTTCGTG 61.577 55.000 0.00 0.00 0.00 4.35
563 566 1.261619 CGATATTTGCTGCGTCCCTTC 59.738 52.381 0.00 0.00 0.00 3.46
583 620 2.171489 GACGTTTCACTTCAGGGCGC 62.171 60.000 0.00 0.00 0.00 6.53
667 716 6.782298 ATAACATCAGCTCTTCAATCATCG 57.218 37.500 0.00 0.00 0.00 3.84
670 726 7.795047 TCCTTATAACATCAGCTCTTCAATCA 58.205 34.615 0.00 0.00 0.00 2.57
817 913 1.366319 AGGGACTCAGCAAGGTCATT 58.634 50.000 5.58 0.00 34.49 2.57
895 1035 5.756347 TCGCTTATGTGTTTGTTCTTGTACT 59.244 36.000 0.00 0.00 0.00 2.73
938 1093 4.118023 CGTCTATCTGTACGTAGCTGAC 57.882 50.000 0.00 0.00 34.48 3.51
998 1161 1.109920 AGCTGGAGCCGACGTCATAT 61.110 55.000 17.16 0.00 43.38 1.78
999 1162 1.725557 GAGCTGGAGCCGACGTCATA 61.726 60.000 17.16 0.00 43.38 2.15
1655 1926 0.251209 GAACCTCACCCCACCTTTCC 60.251 60.000 0.00 0.00 0.00 3.13
2012 2287 2.929043 AGAAATTCCAACCATCCCTCCT 59.071 45.455 0.00 0.00 0.00 3.69
2058 2333 9.720769 ACACAAGTAGCACTTACAACTAATATT 57.279 29.630 0.00 0.00 36.03 1.28
2755 3063 1.134367 CACACGGTCCGATGTATGAGT 59.866 52.381 20.51 0.29 0.00 3.41
2891 3199 5.448162 GCGCATTTCACGTAGATAGAAAAAC 59.552 40.000 0.30 0.00 35.20 2.43
2905 3213 3.266964 TGCTCCTGCGCATTTCAC 58.733 55.556 12.24 0.00 43.34 3.18


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.